chrX-101488839-A-G

Position:

• chrX-101488839-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001256155.3(ARMCX4):​c.250A>G​(p.Arg84Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.69 (19074 hom., 22145 hem., cov: 23)
  • Exomes 𝑓: 0.69 (171939 hom. 235199 hem.)
  • Failed GnomAD Quality Control
• Consequence: ARMCX4 NM_001256155.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395

Genes affected

ARMCX4 (HGNC:28615): (armadillo repeat containing X-linked 4) The product of this gene belongs to the armadillo repeat-containing family of proteins, which interact with other proteins in a variety of cellular processes. The function of this family member is currently unknown. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=3.290057E-5).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMCX4	NM_001256155.3	c.250A>G	p.Arg84Gly	missense_variant	6/6	ENST00000423738.5	NP_001243084.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMCX4	ENST00000423738.5	c.250A>G	p.Arg84Gly	missense_variant	6/6	5	NM_001256155.3	ENSP00000404304	P1

Frequencies

GnomAD3 genomes AF: 0.692 AC: 76393 AN: 110472 Hom.: 19075 Cov.: 23 AF XY: 0.676 AC XY: 22104 AN XY: 32698

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.701

GnomAD3 exomes AF: 0.638 AC: 65472 AN: 102571 Hom.: 13725 AF XY: 0.635 AC XY: 23985 AN XY: 37763

Gnomad AFR exome AF: 0.730

Gnomad AMR exome AF: 0.531

Gnomad ASJ exome AF: 0.724

Gnomad EAS exome AF: 0.458

Gnomad SAS exome AF: 0.537

Gnomad FIN exome AF: 0.684

Gnomad NFE exome AF: 0.724

Gnomad OTH exome AF: 0.667

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.694 AC: 723581 AN: 1042326 Hom.: 171939 Cov.: 49 AF XY: 0.689 AC XY: 235199 AN XY: 341218

Gnomad4 AFR exome AF: 0.731

Gnomad4 AMR exome AF: 0.541

Gnomad4 ASJ exome AF: 0.728

Gnomad4 EAS exome AF: 0.418

Gnomad4 SAS exome AF: 0.544

Gnomad4 FIN exome AF: 0.672

Gnomad4 NFE exome AF: 0.717

Gnomad4 OTH exome AF: 0.686

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.691 AC: 76421 AN: 110530 Hom.: 19074 Cov.: 23 AF XY: 0.676 AC XY: 22145 AN XY: 32766

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.699

Alfa AF: 0.702 Hom.: 23254

Bravo AF: 0.690

TwinsUK AF: 0.710 AC: 2633

ALSPAC AF: 0.715 AC: 2067

ExAC AF: 0.611 AC: 11232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.065
BayesDel_addAF	Benign	-0.87	T
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.80
FATHMM_MKL	Benign	0.0071	N
LIST_S2	Benign	0.19	T
MetaRNN	Benign	0.000033	T
MetaSVM	Benign	-0.94	T
MutationTaster	Benign	1.0	P
PrimateAI	Benign	0.23	T
REVEL	Benign	0.011
Sift4G	Benign	0.59	T
Vest4		0.032
ClinPred		0.0084	T
GERP RS		-1.0
gMVP		0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5951332; hg19: chrX-100743826;